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  • How can I filter out reads who or whose pairs are unmapped in samtools?

    How can I filter out reads who or whose pairs are unmapped in samtools?

    I tried using "samtools view -F 4 -F 8 SAMFILE". However, this command just allows filtering out those whose pairs are unmapped (only "-F 8" is effective).

    I wonder if it is possible to do the job in one command.

  • #2
    Originally posted by maimaiti2008 View Post
    How can I filter out reads who or whose pairs are unmapped in samtools?

    I tried using "samtools view -F 4 -F 8 SAMFILE". However, this command just allows filtering out those whose pairs are unmapped (only "-F 8" is effective).

    I wonder if it is possible to do the job in one command.
    um do them one at a time

    samtools view -bS -F 4 -o OUTBAM_mapped SAMFILE
    samtools view -bS -F 8 -o OUTBAM_unmapped SAMFILE

    you can do "samtools merge" to combine them for analysis if thats what you're after

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